Seems like it's time to either take the time to cut it in manually, reexport from Logic with the proper timecode if possible, or, do the following cheat.

Put the long clip in a new sequence that you manually set to the precise timecode that long clip starts at, then export the audio with the new timecode. Then you should be able to figure it out from there.

In the future, you should move all the audio from the bad clip to its own track, then export only that track, fix that in Logic, then replace the entire track.

David Roth Weiss
Director/Editor/Colorist
David Weiss Productions

David is a Creative COW contributing editor and a forum host of the Apple Final Cut Pro forum.

In this case, after thinking things through, I just went through my original process once more and it worked. The difference was that last time it didn't let me force the reconnection. This time, after notice about missing rate and media start/end data, I was able to force a connection and this did the job.